You're right that the top of the page is not where ads should go. But
sites don't have much of a choice. On paper, you can see the whole page
at once, so ads can go anywhere on a page and still be effective. Web
pages are usually long and narrow, so you have to scroll to get to the
bottom. Many people won't scroll that far. And since paper provides a
sense of context (several pages are usually bound together), ads can go
on their own page and still get seen. On the Web, there's much less
context.

Your idea about putting ads on the side seems to be popular with HotWired
and their subsidiary Suck. I particularly like the way ads are set up on
Packet.

The idea of advertisers reimbursing people for looking at ads is not new,
however it is part of a larger, variable-rate pricing scheme that has to
be in place for it to work. An important part of this is that the
reimbursment need not be in US dollars or any other kind of "real"
currency. On the Internet, anything that you can trade is
currency.

Ideas are being floated on the Cypherpunks mailing list that anonymous
remailers should require a form of postage called "hashcash". Hashcash
has no value in the real world, but to generate a certain amount of
hashcash requires a certain amount of processing time. So you have to run
a program on your computer that generates hashcash, and you send the
hashcash with the email. The amount of hashcash you include is
proportional to your abuse of the server. Spammers would have to have
huge render farms of computers to generate enough postage for their mail.